Vitamin D has an important role in bone metabolism but recently has been recognized as an immunoregulator, and this has led to investigations on the effect of Vitamin D supplementation in various autoimmune diseases and its anti-inflammatory effects. There is some evidence that Vitamin D can regulate gastrointestinal inflammation. In addition, previous studies have shown that Vitamin D can affect the gut microbiome. The aim of this review is to evaluate the effect of Vitamin D on inflammatory processes, especially its relation to the inflammatory bowel disease (IBD) and gut microbiome. There is some evidence that Vitamin D can regulate gastrointestinal inflammation, with epidemiological studies showing that individuals with higher serum Vitamin D have a lower incidence of IBD, particularly Crohn's disease. Vitamin D changes transcription of cathelicidin and DEFB4 (defensin, beta 4) that can affect the gut microbiome. Several cell types of the immune system express Vitamin D receptor, and hence the use of Vitamin D in immune regulation has some potential. Furthermore, Vitamin D deficiency leads to dysbiosis of gut microbiome and reported to cause severe colitis. Vitamin D supplementation is low cost and available and can be a therapeutic option.